Imports and custom functions

In [2]:
import pandas as pd
import seaborn as sns
import plotly
import plotly.express as px
import plotly.graph_objects as go
plotly.offline.init_notebook_mode(connected=True)
import matplotlib.pyplot as plt
In [3]:
def prepare_df(df_path, df_name):

    """Read in information from dataframe"""

    # read in df1
    df = pd.read_csv(df_path, header=0, sep="\t")
    # Mark significants
    df["Significant"]  = "No"
    df.loc[(df["FDR"] < 0.05) & (df["logCPM"]>2), "Significant"] = "FDR<0.05\nlogCPM>2"
    # set id as index
    df.set_index("id", inplace=True)
    # rename columns
    df.columns = df.columns + "_" + df_name
    # reset index
    df.reset_index(inplace=True)

    return df
In [4]:
def plot_MA(df, df_name):

    """Plot MA"""

    sns.set(font_scale=2)
    sns_plot = sns.lmplot(x=f"logCPM_{df_name}",
                          y=f"logFC_{df_name}",
                          data=df,
                          fit_reg=False,
                          hue=f"Significant_{df_name}",
                          palette=["black", "red"],
                          height=15,
                          aspect=1)
    ax = plt.gca()
    ax.set_title(f"MA plot for {df_name}")
In [5]:
def merge_df(df_1, df_2):
    
    """Merge dataframes"""
    
    df = pd.merge(df_1, df_2, on="id")
    df["Significant"] = "No"
    return df
In [6]:
def plot_FC_correlation(df, FC_1_name, FC_2_name, hue, hue_order):

    """Plot correlation between FCs"""

    sns.set(font_scale=2)
    sns_plot = sns.lmplot(x=f"logFC_{FC_1_name}",
                          y=f"logFC_{FC_2_name}",
                          data=df,
                          fit_reg=False,
                          hue=hue,
                          hue_order=hue_order,
                          palette=["black", "yellow", "blue", "green"],
                          height=15,
                          aspect=1)
    ax = plt.gca()
    ax.set_title(f"FCs between {FC_1_name} and {FC_2_name}")
In [7]:
def compare(df_1_path, df_2_path, df_1_name, df_2_name):
    
    "Combine multiple functions"
    
    df_1 = prepare_df(df_1_path, df_1_name)
    plot_MA(df_1, df_1_name)
    df_2 = prepare_df(df_2_path, df_2_name)
    plot_MA(df_2, df_2_name)
    
    df_merged = merge_df(df_1, df_2)
    
#     plot_FC_correlation(df_merged, df_1_name, df_2_name, hue="Significant")
#     plot_FC_correlation(df_merged, df_1_name, df_2_name, hue="Significant_" + df_1_name)
#     plot_FC_correlation(df_merged, df_1_name, df_2_name, hue="Significant_" + df_2_name)
    
    return df_merged

Input files

In [8]:
ip_path = "../WAGO_3_IP/results/DE__N2_Input_Rpph__N2_xf119_Rpph/plot_small_RNAs/22G.tsv"
ip_name = "WAGO-3"

Dpf_3_null_path = "../small_RNA_seq_15_C/results/DE__WT_dpf3__Dpf_3_null/plot_small_RNAs/22G.tsv"
Dpf_3_null_name = "Dpf_3_null"

Dpf_3_S784A_path = "../small_RNA_seq_15_C/results/DE__WT_dpf3__Dpf_3_S784A//plot_small_RNAs/22G.tsv"
Dpf_3_S784A_name = "Dpf_3_S784A"

mut_2_path = "../small_RNA_seq_15_C/results/DE__WT_other__mut_2/plot_small_RNAs/22G.tsv"
mut_2_name = "mut_2"

mut_7_path = "../small_RNA_seq_15_C/results/DE__WT_other__mut_7/plot_small_RNAs/22G.tsv"
mut_7_name = "mut_7"

Dpf_3_null_first_path = "../small_RNA_seq_15_C/results/DE__WT_dpf3_first__Dpf_3_null/plot_small_RNAs/22G.tsv"
Dpf_3_null_first_name = "Dpf_3_null_first"

Dpf_3_S784A_second_path = "../small_RNA_seq_15_C/results/DE__WT_dpf3_second__Dpf_3_S784A/plot_small_RNAs/22G.tsv"
Dpf_3_S784A_second_name = "Dpf_3_S784A_second"

Dpf_3_null_old_path = "../small_RNA_seq_25_C/results/DE__WT__dpf_3_delta/plot_small_RNAs/22G.tsv"
Dpf_3_null_old_name = "Dpf_3_null_old"

dpf_3S784A_old_path = "../small_RNA_seq_25_C/results/DE__WT__dpf_3S784A/plot_small_RNAs/22G.tsv"
dpf_3S784A_old_name = "Dpf_3_S784A_old"

ip_wago_9_path = "../WAGO_9_IP/results/DE__wago-9_input__wago-9_IP/plot_small_RNAs/22G.tsv"
ip_wago_9_name = "WAGO-9"

ip_csr_1_path = "../csr_1_IP/results/DE__csr-1_input__csr-1_IP/plot_small_RNAs/22G.tsv"
ip_csr_1_name = "csr-1"

Comparisons

1. IP vs Dpf_3_null

In [9]:
df_1_path = ip_path
df_2_path = Dpf_3_null_path
df_1_name = ip_name
df_2_name = Dpf_3_null_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[9]:
Significant
No 217464
FDR_WAGO-3<0.05\nlogCPM_WAGO-3>2 10889
FDR_WAGO-3<0.05\nFDR_Dpf_3_null<0.05\nlogCPM_WAGO-3>2\nlogCPM_Dpf_3_null>2 1824
FDR_Dpf_3_null<0.05\nlogCPM_Dpf_3_null>2 1446

2. IP vs Dpf_3_S784A

In [10]:
df_1_path = ip_path
df_2_path = Dpf_3_S784A_path
df_1_name = ip_name
df_2_name = Dpf_3_S784A_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[10]:
Significant
No 202355
FDR_WAGO-3<0.05\nlogCPM_WAGO-3>2 10468
FDR_WAGO-3<0.05\nFDR_Dpf_3_S784A<0.05\nlogCPM_WAGO-3>2\nlogCPM_Dpf_3_S784A>2 2185
FDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_S784A>2 1829

3. IP vs mut_2

In [11]:
df_1_path = ip_path
df_2_path = mut_2_path
df_1_name = ip_name
df_2_name = mut_2_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[11]:
Significant
No 181721
FDR_WAGO-3<0.05\nlogCPM_WAGO-3>2 8851
FDR_mut_2<0.05\nlogCPM_mut_2>2 3292
FDR_WAGO-3<0.05\nFDR_mut_2<0.05\nlogCPM_WAGO-3>2\nlogCPM_mut_2>2 3235

4. IP vs mut_7

In [12]:
df_1_path = ip_path
df_2_path = mut_7_path
df_1_name = ip_name
df_2_name = mut_7_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[12]:
Significant
No 187787
FDR_WAGO-3<0.05\nlogCPM_WAGO-3>2 9491
FDR_WAGO-3<0.05\nFDR_mut_7<0.05\nlogCPM_WAGO-3>2\nlogCPM_mut_7>2 2579
FDR_mut_7<0.05\nlogCPM_mut_7>2 2090

5.a. Dpf_3_null vs Dpf_3_S784A with same WTs (It's wrong but I leave it, just to see the differences)

In [13]:
df_1_path = Dpf_3_null_path
df_2_path = Dpf_3_S784A_path
df_1_name = Dpf_3_null_name
df_2_name = Dpf_3_S784A_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [14]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[14]:
Significant
No 356378
FDR_Dpf_3_null<0.05\nFDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_null>2\nlogCPM_Dpf_3_S784A>2 3073
FDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_S784A>2 986
FDR_Dpf_3_null<0.05\nlogCPM_Dpf_3_null>2 235

5.b. Dpf_3_null vs Dpf_3_S784A with different WTs

In [15]:
df_1_path = Dpf_3_null_first_path
df_2_path = Dpf_3_S784A_second_path
df_1_name = Dpf_3_null_first_name
df_2_name = Dpf_3_S784A_second_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [16]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[16]:
Significant
No 144114
FDR_Dpf_3_S784A_second<0.05\nlogCPM_Dpf_3_S784A_second>2 1519
FDR_Dpf_3_null_first<0.05\nFDR_Dpf_3_S784A_second<0.05\nlogCPM_Dpf_3_null_first>2\nlogCPM_Dpf_3_S784A_second>2 1513
FDR_Dpf_3_null_first<0.05\nlogCPM_Dpf_3_null_first>2 212

6. Dpf_3_null vs mut_2

In [17]:
df_1_path = Dpf_3_null_path
df_2_path = mut_2_path
df_1_name = Dpf_3_null_name
df_2_name = mut_2_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [18]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[18]:
Significant
No 175005
FDR_mut_2<0.05\nlogCPM_mut_2>2 3795
FDR_Dpf_3_null<0.05\nFDR_mut_2<0.05\nlogCPM_Dpf_3_null>2\nlogCPM_mut_2>2 2794
FDR_Dpf_3_null<0.05\nlogCPM_Dpf_3_null>2 514

7. Dpf_3_null vs mut_7

In [19]:
df_1_path = Dpf_3_null_path
df_2_path = mut_7_path
df_1_name = Dpf_3_null_name
df_2_name = mut_7_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [20]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[20]:
Significant
No 181141
FDR_Dpf_3_null<0.05\nFDR_mut_7<0.05\nlogCPM_Dpf_3_null>2\nlogCPM_mut_7>2 2372
FDR_mut_7<0.05\nlogCPM_mut_7>2 2339
FDR_Dpf_3_null<0.05\nlogCPM_Dpf_3_null>2 936

8. Dpf_3_Dpf_3_S784A vs mut_2

In [21]:
df_1_path = Dpf_3_S784A_path
df_2_path = mut_2_path
df_1_name = Dpf_3_S784A_name
df_2_name = mut_2_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [22]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[22]:
Significant
No 164457
FDR_Dpf_3_S784A<0.05\nFDR_mut_2<0.05\nlogCPM_Dpf_3_S784A>2\nlogCPM_mut_2>2 3337
FDR_mut_2<0.05\nlogCPM_mut_2>2 3238
FDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_S784A>2 722

9. Dpf_3_Dpf_3_S784A vs mut_7

In [23]:
df_1_path = Dpf_3_S784A_path
df_2_path = mut_7_path
df_1_name = Dpf_3_S784A_name
df_2_name = mut_7_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [24]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[24]:
Significant
No 169787
FDR_Dpf_3_S784A<0.05\nFDR_mut_7<0.05\nlogCPM_Dpf_3_S784A>2\nlogCPM_mut_7>2 2824
FDR_mut_7<0.05\nlogCPM_mut_7>2 1877
FDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_S784A>2 1236

10. Dpf_3_null vs Dpf_3_null_old

In [25]:
df_1_path = Dpf_3_null_path
df_2_path = Dpf_3_null_old_path
df_1_name = Dpf_3_null_name
df_2_name = Dpf_3_null_old_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [26]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[26]:
Significant
No 311859
FDR_Dpf_3_null_old<0.05\nlogCPM_Dpf_3_null_old>2 2356
FDR_Dpf_3_null<0.05\nlogCPM_Dpf_3_null>2 2210
FDR_Dpf_3_null<0.05\nFDR_Dpf_3_null_old<0.05\nlogCPM_Dpf_3_null>2\nlogCPM_Dpf_3_null_old>2 1090

11. Dpf_3_Dpf_3_S784A vs Dpf_3_Dpf_3_S784A old

In [27]:
df_1_path = Dpf_3_S784A_path
df_2_path = dpf_3S784A_old_path
df_1_name = Dpf_3_S784A_name
df_2_name = dpf_3S784A_old_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)
In [28]:
df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[28]:
Significant
No 286729
FDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_S784A>2 2815
FDR_Dpf_3_S784A_old<0.05\nlogCPM_Dpf_3_S784A_old>2 2109
FDR_Dpf_3_S784A<0.05\nFDR_Dpf_3_S784A_old<0.05\nlogCPM_Dpf_3_S784A>2\nlogCPM_Dpf_3_S784A_old>2 1235

12. IP WAGO-9 vs Dpf_3_null

In [29]:
df_1_path = ip_wago_9_path
df_2_path = Dpf_3_null_path
df_1_name = ip_wago_9_name
df_2_name = Dpf_3_null_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[29]:
Significant
No 279584
FDR_WAGO-9<0.05\nlogCPM_WAGO-9>2 6507
FDR_Dpf_3_null<0.05\nlogCPM_Dpf_3_null>2 2689
FDR_WAGO-9<0.05\nFDR_Dpf_3_null<0.05\nlogCPM_WAGO-9>2\nlogCPM_Dpf_3_null>2 601

13. IP WAGO-9 vs Dpf_3_S784A

In [30]:
df_1_path = ip_wago_9_path
df_2_path = Dpf_3_S784A_path
df_1_name = ip_wago_9_name
df_2_name = Dpf_3_S784A_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[30]:
Significant
No 256682
FDR_WAGO-9<0.05\nlogCPM_WAGO-9>2 6261
FDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_S784A>2 3243
FDR_WAGO-9<0.05\nFDR_Dpf_3_S784A<0.05\nlogCPM_WAGO-9>2\nlogCPM_Dpf_3_S784A>2 792

14. IP WAGO-9 vs mut_2

In [31]:
df_1_path = ip_wago_9_path
df_2_path = mut_2_path
df_1_name = ip_wago_9_name
df_2_name = mut_2_name


df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[31]:
Significant
No 237878
FDR_WAGO-9<0.05\nlogCPM_WAGO-9>2 5005
FDR_mut_2<0.05\nlogCPM_mut_2>2 4844
FDR_WAGO-9<0.05\nFDR_mut_2<0.05\nlogCPM_WAGO-9>2\nlogCPM_mut_2>2 1733

15. IP WAGO-9 vs mut_7

In [33]:
df_1_path = ip_wago_9_path
df_2_path = mut_7_path
df_1_name = ip_wago_9_name
df_2_name = mut_7_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[33]:
Significant
No 247105
FDR_WAGO-9<0.05\nlogCPM_WAGO-9>2 5337
FDR_mut_7<0.05\nlogCPM_mut_7>2 3321
FDR_WAGO-9<0.05\nFDR_mut_7<0.05\nlogCPM_WAGO-9>2\nlogCPM_mut_7>2 1385

16. IP crs-1 vs Dpf_3_null

In [34]:
df_1_path = ip_csr_1_path
df_2_path = Dpf_3_null_path
df_1_name = ip_csr_1_name
df_2_name = Dpf_3_null_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[34]:
Significant
No 293722
FDR_Dpf_3_null<0.05\nlogCPM_Dpf_3_null>2 3153
FDR_csr-1<0.05\nlogCPM_csr-1>2 1725
FDR_csr-1<0.05\nFDR_Dpf_3_null<0.05\nlogCPM_csr-1>2\nlogCPM_Dpf_3_null>2 149

17. IP crs-1 vs Dpf_3_S784A

In [36]:
df_1_path = ip_csr_1_path
df_2_path = Dpf_3_S784A_path
df_1_name = ip_csr_1_name
df_2_name = Dpf_3_S784A_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[36]:
Significant
No 269759
FDR_Dpf_3_S784A<0.05\nlogCPM_Dpf_3_S784A>2 3857
FDR_csr-1<0.05\nlogCPM_csr-1>2 1636
FDR_csr-1<0.05\nFDR_Dpf_3_S784A<0.05\nlogCPM_csr-1>2\nlogCPM_Dpf_3_S784A>2 197

18. IP crs-1 vs mut_2

In [37]:
df_1_path = ip_csr_1_path
df_2_path = mut_2_path
df_1_name = ip_csr_1_name
df_2_name = mut_2_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[37]:
Significant
No 245878
FDR_mut_2<0.05\nlogCPM_mut_2>2 6264
FDR_csr-1<0.05\nlogCPM_csr-1>2 1428
FDR_csr-1<0.05\nFDR_mut_2<0.05\nlogCPM_csr-1>2\nlogCPM_mut_2>2 325

19. IP crs-1 vs mut_7

In [38]:
df_1_path = ip_csr_1_path
df_2_path = mut_7_path
df_1_name = ip_csr_1_name
df_2_name = mut_7_name

df_all = compare(df_1_path, df_2_path, df_1_name, df_2_name)

df_all["Significant"] = "No"

df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2),
            "Significant"] = f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2"


df_all.loc[(df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_2_name}"]>2),
            "Significant"] = f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2"


df_all.loc[(df_all[f"FDR_{df_1_name}"]<0.05) & 
           (df_all[f"FDR_{df_2_name}"]<0.05) &
           (df_all[f"logCPM_{df_1_name}"]>2) &
           (df_all[f"logCPM_{df_2_name}"]>2)
           , "Significant"] = f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"

plot_FC_correlation(df_all, df_1_name, df_2_name, hue="Significant", hue_order=["No", f"FDR_{df_1_name}<0.05\nlogCPM_{df_1_name}>2", f"FDR_{df_2_name}<0.05\nlogCPM_{df_2_name}>2", f"FDR_{df_1_name}<0.05\nFDR_{df_2_name}<0.05\nlogCPM_{df_1_name}>2\nlogCPM_{df_2_name}>2"])

pd.DataFrame(df_all["Significant"].value_counts())
Out[38]:
Significant
No 256282
FDR_mut_7<0.05\nlogCPM_mut_7>2 4456
FDR_csr-1<0.05\nlogCPM_csr-1>2 1498
FDR_csr-1<0.05\nFDR_mut_7<0.05\nlogCPM_csr-1>2\nlogCPM_mut_7>2 252